Merge pull request #484 from cmu-phil/joebugfixes

joebugfixes
cmu-phil · Jun 19, 2017 · c545c4f · c545c4f
2 parents ef8cdc8 + 40b2b94
commit c545c4f
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Showing 24 changed files with 231 additions and 56 deletions.
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/Tetrad.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/Tetrad.java
@@ -160,12 +160,9 @@ private void launchFrame() {
         this.frame = new JFrame(this.mainTitle) {
             public Dimension getPreferredSize() {
                 Dimension size = Toolkit.getDefaultToolkit().getScreenSize();
-                double width = size.getWidth();
-                double height = size.getHeight();
-                double minSize = Math.min(width, height);
-
-                height = minSize / 2;
-                width = minSize * 0.75;
+                double minLength = Math.min(size.getWidth(), size.getHeight());
+                double height = minLength * 0.8;
+                double width = height * (4.0 / 3);
 
                 return new Dimension((int) width, (int) height);
 //                return Toolkit.getDefaultToolkit().getScreenSize();
@@ -195,6 +192,7 @@ public Dimension getPreferredSize() {
 
         getFrame().setContentPane(getDesktop());
         getFrame().pack();
+        getFrame().setLocationRelativeTo(null);
 
         // This doesn't let the user resize the main window.
 //        getFrame().setExtendedState(Frame.MAXIMIZED_BOTH);

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/GeneralAlgorithmEditor.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/GeneralAlgorithmEditor.java
@@ -99,6 +99,12 @@
  */
 public class GeneralAlgorithmEditor extends JPanel implements FinalizingEditor {
 
+    // Note: When adding an algorithm, make sure you do all of the following:
+    // 1. Add a new type to private enum AlgName.
+    // 2. Add a desription for it to final List<AlgorithmDescription> descriptions.
+    // 3. In private Algorithm getAlgorithm, add a new case to the switch statement returning
+    // an instance of the algorithm.
+
     private static final long serialVersionUID = -5719467682865706447L;
 
     private final HashMap<AlgName, AlgorithmDescription> mappedDescriptions;

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/SimulationEditor.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/SimulationEditor.java
@@ -34,6 +34,7 @@
 import edu.cmu.tetradapp.model.KnowledgeEditable;
 import edu.cmu.tetradapp.model.Simulation;
 import edu.cmu.tetradapp.util.WatchedProcess;
+
 import java.awt.*;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
@@ -63,6 +64,7 @@ public final class SimulationEditor extends JPanel implements KnowledgeEditable,
     private final JComboBox<String> simulationsDropdown = new JComboBox<>();
 
     //==========================CONSTUCTORS===============================//
+
     /**
      * Constructs the data editor with an empty list of data displays.
      */
@@ -104,11 +106,11 @@ public SimulationEditor(final Simulation simulation) {
         tabbedPane.setPreferredSize(new Dimension(900, 600));
 
         final String[] graphItems = new String[]{
-            "Random Foward DAG",
-            "Scale Free DAG",
-            "Cyclic, constructed from small loops",
-            "Random One Factor MIM",
-            "Random Two Factor MIM"
+                "Random Foward DAG",
+                "Scale Free DAG",
+                "Cyclic, constructed from small loops",
+                "Random One Factor MIM",
+                "Random Two Factor MIM"
         };
 
         for (String item : graphItems) {
@@ -242,15 +244,15 @@ public void actionPerformed(ActionEvent e) {
                     if (thisOne == null) {
                         JOptionPane.showMessageDialog((SimulationEditor.this),
                                 "That file was not a simulation, and none of its subdirectories was either. "
-                                + "\nNeed a directory with a 'data' subdirectory, a 'graph' subdirectory, "
-                                + "\nand a 'parameters.txt' file.");
+                                        + "\nNeed a directory with a 'data' subdirectory, a 'graph' subdirectory, "
+                                        + "\nand a 'parameters.txt' file.");
                         return;
                     }
 
                     if (count > 1) {
                         JOptionPane.showMessageDialog((SimulationEditor.this),
                                 "More than one subdirectory of that directory was a simulation; please select "
-                                + "\none of the subdirectories.");
+                                        + "\none of the subdirectories.");
                         return;
                     }
 
@@ -410,6 +412,8 @@ private void resetPanel(Simulation simulation, String[] graphItems, String[] sim
                 } else if (simulationItem.equals(simulationItems[3])) {
                     simulation.setSimulation(new LeeHastieSimulation(randomGraph), simulation.getParams());
                 } else if (simulationItem.equals(simulationItems[4])) {
+                    simulation.setSimulation(new ConditionalGaussianSimulation(randomGraph), simulation.getParams());
+                } else if (simulationItem.equals(simulationItems[5])) {
                     simulation.setSimulation(new TimeSeriesSemSimulation(randomGraph), simulation.getParams());
                 } else {
                     throw new IllegalArgumentException("Unrecognized simulation type: " + simulationItem);
@@ -436,6 +440,8 @@ private void resetPanel(Simulation simulation, String[] graphItems, String[] sim
                 } else if (simulationItem.equals(simulationItems[3])) {
                     simulation.setSimulation(new LeeHastieSimulation(randomGraph), simulation.getParams());
                 } else if (simulationItem.equals(simulationItems[4])) {
+                    simulation.setSimulation(new ConditionalGaussianSimulation(randomGraph), simulation.getParams());
+                } else if (simulationItem.equals(simulationItems[5])) {
                     simulation.setSimulation(new TimeSeriesSemSimulation(randomGraph), simulation.getParams());
 //                } else if (simulationItem.equals(simulationItems[6])) {
 //                    simulation.setSimulation(new BooleanGlassSimulation(randomGraph), simulation.getParams());
@@ -456,25 +462,25 @@ private String[] getSimulationItems(Simulation simulation) {
         if (simulation.isFixedSimulation()) {
             if (simulation.getSimulation() instanceof BayesNetSimulation) {
                 simulationItems = new String[]{
-                    "Bayes net",};
+                        "Bayes net",};
             } else if (simulation.getSimulation() instanceof SemSimulation) {
                 simulationItems = new String[]{
-                    "Structural Equation Model"
+                        "Structural Equation Model"
                 };
             } else if (simulation.getSimulation() instanceof LinearFisherModel) {
                 simulationItems = new String[]{
-                    "Linear Fisher Model"
+                        "Linear Fisher Model"
                 };
             } else if (simulation.getSimulation() instanceof StandardizedSemSimulation) {
                 simulationItems = new String[]{
-                    "Standardized Structural Equation Model"
+                        "Standardized Structural Equation Model"
                 };
             } else if (simulation.getSimulation() instanceof GeneralSemSimulation) {
                 simulationItems = new String[]{
-                    "General Structural Equation Model",};
+                        "General Structural Equation Model",};
             } else if (simulation.getSimulation() instanceof LoadContinuousDataAndGraphs) {
                 simulationItems = new String[]{
-                    "Loaded From Files",};
+                        "Loaded From Files",};
             } else {
                 throw new IllegalStateException("Not expecting that model type: "
                         + simulation.getSimulation().getClass());
@@ -487,21 +493,23 @@ private String[] getSimulationItems(Simulation simulation) {
 //            } else
             if (simulation.getSourceGraph() != null) {
                 simulationItems = new String[]{
-                    "Bayes net",
-                    "Structural Equation Model",
-                    "Linear Fisher Model",
-                    //                        "General Structural Equation Model Special",
-                    "Lee & Hastie",
-                    "Time Series"
+                        "Bayes net",
+                        "Structural Equation Model",
+                        "Linear Fisher Model",
+                        //                        "General Structural Equation Model Special",
+                        "Lee & Hastie",
+                        "Conditional Gaussian",
+                        "Time Series"
                 };
             } else {
                 simulationItems = new String[]{
-                    "Bayes net",
-                    "Structural Equation Model",
-                    "Linear Fisher Model",
-                    //                        "General Structural Equation Model Special",
-                    "Lee & Hastie",
-                    "Time Series", //                        "Boolean Glass"
+                        "Bayes net",
+                        "Structural Equation Model",
+                        "Linear Fisher Model",
+                        //                        "General Structural Equation Model Special",
+                        "Lee & Hastie",
+                        "Conditional Gaussian",
+                        "Time Series", //                        "Boolean Glass"
                 };
             }
         }
@@ -510,8 +518,8 @@ private String[] getSimulationItems(Simulation simulation) {
     }
 
     private Box getParametersPane(Simulation _simulation,
-            edu.cmu.tetrad.algcomparison.simulation.Simulation simulation,
-            Parameters parameters) {
+                                  edu.cmu.tetrad.algcomparison.simulation.Simulation simulation,
+                                  Parameters parameters) {
         JScrollPane scroll;
 
         if (simulation != null) {

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/KnowledgeBoxModel.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/KnowledgeBoxModel.java
@@ -27,6 +27,7 @@
 import edu.cmu.tetrad.graph.EdgeListGraph;
 import edu.cmu.tetrad.graph.Graph;
 import edu.cmu.tetrad.graph.Node;
+import edu.cmu.tetrad.graph.NodeType;
 import edu.cmu.tetrad.session.ParamsResettable;
 import edu.cmu.tetrad.session.SessionModel;
 import edu.cmu.tetrad.util.Parameters;
@@ -78,8 +79,15 @@ public KnowledgeBoxModel(KnowledgeBoxInput[] inputs, Parameters params) {
         SortedSet<String> variableNames = new TreeSet<>();
 
         for (KnowledgeBoxInput input : inputs) {
-            variableNodes.addAll(input.getVariables());
-            variableNames.addAll(input.getVariableNames());
+            for (Node node : input.getVariables()) {
+                if (node.getNodeType() == NodeType.MEASURED) {
+                    variableNodes.add(node);
+                    variableNames.add(node.getName());
+                }
+            }
+
+//            variableNodes.addAll(input.getVariables());
+//            variableNames.addAll(input.getVariableNames());
         }
 
         this.variables = new ArrayList<>(variableNodes);

diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pattern/FgesMb.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pattern/FgesMb.java
@@ -44,7 +44,11 @@ public Graph search(DataModel dataSet, Parameters parameters) {
             initial = initialGraph.search(dataSet, parameters);
         }
 
-        Score score = this.score.getScore(DataUtils.getContinuousDataSet(dataSet), parameters);
+//        Score score = this.score.getScore(DataUtils.getContinuousDataSet(dataSet), parameters);
+//
+//        Score score =
+
+        Score score = this.score.getScore(dataSet, parameters);
         edu.cmu.tetrad.search.FgesMb search = new edu.cmu.tetrad.search.FgesMb(score);
         search.setFaithfulnessAssumed(parameters.getBoolean("faithfulnessAssumed"));
         search.setKnowledge(knowledge);
@@ -54,7 +58,7 @@ public Graph search(DataModel dataSet, Parameters parameters) {
         }
 
         this.targetName = parameters.getString("targetName");
-        Node target = score.getVariable(targetName);
+        Node target = this.score.getVariable(targetName);
 
         return search.search(Collections.singletonList(target));
     }

diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/score/BdeuScore.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/score/BdeuScore.java
@@ -2,6 +2,7 @@
 
 import edu.cmu.tetrad.data.DataModel;
 import edu.cmu.tetrad.data.DataUtils;
+import edu.cmu.tetrad.graph.Node;
 import edu.cmu.tetrad.util.Parameters;
 import edu.cmu.tetrad.data.DataType;
 import edu.cmu.tetrad.search.Score;
@@ -16,9 +17,11 @@
  */
 public class BdeuScore implements ScoreWrapper {
     static final long serialVersionUID = 23L;
+    private DataModel dataSet;
 
     @Override
     public Score getScore(DataModel dataSet, Parameters parameters) {
+        this.dataSet = dataSet;
         edu.cmu.tetrad.search.BDeuScore score
                 = new edu.cmu.tetrad.search.BDeuScore(DataUtils.getDiscreteDataSet(dataSet));
         score.setSamplePrior(parameters.getDouble("samplePrior"));
@@ -43,4 +46,9 @@ public List<String> getParameters() {
         parameters.add("structurePrior");
         return parameters;
     }
+
+    @Override
+    public Node getVariable(String name) {
+        return dataSet.getVariable(name);
+    }
 }
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/score/ConditionalGaussianBicScore.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/score/ConditionalGaussianBicScore.java
@@ -2,6 +2,7 @@
 
 import edu.cmu.tetrad.data.DataModel;
 import edu.cmu.tetrad.data.DataUtils;
+import edu.cmu.tetrad.graph.Node;
 import edu.cmu.tetrad.util.Parameters;
 import edu.cmu.tetrad.data.DataType;
 import edu.cmu.tetrad.search.ConditionalGaussianScore;
@@ -18,9 +19,11 @@
  */
 public class  ConditionalGaussianBicScore implements ScoreWrapper, Experimental {
     static final long serialVersionUID = 23L;
+    private DataModel dataSet;
 
     @Override
     public Score getScore(DataModel dataSet, Parameters parameters) {
+        this.dataSet = dataSet;
         final ConditionalGaussianScore conditionalGaussianScore
                 = new ConditionalGaussianScore(DataUtils.getMixedDataSet(dataSet), parameters.getDouble("structurePrior"), parameters.getBoolean("discretize"));
         conditionalGaussianScore.setPenaltyDiscount(parameters.getDouble("penaltyDiscount"));
@@ -48,4 +51,9 @@ public List<String> getParameters() {
         parameters.add("discretize");
         return parameters;
     }
+
+    @Override
+    public Node getVariable(String name) {
+        return dataSet.getVariable(name);
+    }
 }
diff --git a/...ib/src/main/java/edu/cmu/tetrad/algcomparison/score/ConditionalGaussianOtherBicScore.java b/...ib/src/main/java/edu/cmu/tetrad/algcomparison/score/ConditionalGaussianOtherBicScore.java
@@ -3,6 +3,7 @@
 import edu.cmu.tetrad.data.DataModel;
 import edu.cmu.tetrad.data.DataType;
 import edu.cmu.tetrad.data.DataUtils;
+import edu.cmu.tetrad.graph.Node;
 import edu.cmu.tetrad.search.ConditionalGaussianOtherScore;
 import edu.cmu.tetrad.search.ConditionalGaussianScore;
 import edu.cmu.tetrad.search.Score;
@@ -19,9 +20,11 @@
  */
 public class ConditionalGaussianOtherBicScore implements ScoreWrapper, Experimental {
     static final long serialVersionUID = 23L;
+    private DataModel dataSet;
 
     @Override
     public Score getScore(DataModel dataSet, Parameters parameters) {
+        this.dataSet = dataSet;
         final ConditionalGaussianOtherScore conditionalGaussianScore
                 = new ConditionalGaussianOtherScore(DataUtils.getMixedDataSet(dataSet), parameters.getDouble("structurePrior"), parameters.getBoolean("discretize"));
         conditionalGaussianScore.setPenaltyDiscount(parameters.getDouble("penaltyDiscount"));
@@ -49,4 +52,9 @@ public List<String> getParameters() {
         parameters.add("discretize");
         return parameters;
     }
+
+    @Override
+    public Node getVariable(String name) {
+        return dataSet.getVariable(name);
+    }
 }
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/score/DiscreteBicScore.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/score/DiscreteBicScore.java
@@ -2,6 +2,7 @@
 
 import edu.cmu.tetrad.data.DataModel;
 import edu.cmu.tetrad.data.DataUtils;
+import edu.cmu.tetrad.graph.Node;
 import edu.cmu.tetrad.util.Parameters;
 import edu.cmu.tetrad.data.DataType;
 import edu.cmu.tetrad.search.Score;
@@ -16,9 +17,11 @@
  */
 public class DiscreteBicScore implements ScoreWrapper {
     static final long serialVersionUID = 23L;
+    private DataModel dataSet;
 
     @Override
     public Score getScore(DataModel dataSet, Parameters parameters) {
+        this.dataSet = dataSet;
         edu.cmu.tetrad.search.BicScore score
                 = new edu.cmu.tetrad.search.BicScore(DataUtils.getDiscreteDataSet(dataSet));
         score.setPenaltyDiscount(parameters.getDouble("penaltyDiscount"));
@@ -41,4 +44,9 @@ public List<String> getParameters() {
         paramDescriptions.add("penaltyDiscount");
         return paramDescriptions;
     }
+
+    @Override
+    public Node getVariable(String name) {
+        return dataSet.getVariable(name);
+    }
 }
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/score/DseparationScore.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/score/DseparationScore.java
@@ -3,6 +3,7 @@
 import edu.cmu.tetrad.algcomparison.graph.RandomGraph;
 import edu.cmu.tetrad.data.DataModel;
 import edu.cmu.tetrad.data.DataType;
+import edu.cmu.tetrad.graph.Node;
 import edu.cmu.tetrad.search.*;
 import edu.cmu.tetrad.util.Parameters;
 
@@ -17,13 +18,15 @@
 public class DseparationScore implements ScoreWrapper {
     static final long serialVersionUID = 23L;
     private final RandomGraph randomGraph;
+    private DataModel dataSet;
 
     public DseparationScore(RandomGraph randomGraph) {
         this.randomGraph = randomGraph;
     }
 
     @Override
     public Score getScore(DataModel dataSet, Parameters parameters) {
+        this.dataSet = dataSet;
         if (dataSet == null) {
             return new GraphScore(randomGraph.createGraph(parameters));
         } else {
@@ -46,4 +49,9 @@ public List<String> getParameters() {
         return new ArrayList<>();
     }
 
+    @Override
+    public Node getVariable(String name) {
+        return dataSet.getVariable(name);
+    }
+
 }